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- PDB-7jyv: Crystal Structure of HLA A*2402 in complex with YFSPIRVTF, an 9-m... -

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Basic information

Entry
Database: PDB / ID: 7jyv
TitleCrystal Structure of HLA A*2402 in complex with YFSPIRVTF, an 9-mer influenza epitope
Components
  • Beta-2-microglobulin
  • MHC class I antigen
  • NP peptide from influenza, YFSPIRVTF
KeywordsIMMUNE SYSTEM / HLA A*2402 / influenza virus / TCR / T cell
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / negative regulation of iron ion transport / lumenal side of endoplasmic reticulum membrane / T cell mediated cytotoxicity / cellular response to iron(III) ion ...antigen processing and presentation of peptide antigen via MHC class I / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / negative regulation of iron ion transport / lumenal side of endoplasmic reticulum membrane / T cell mediated cytotoxicity / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / transferrin transport / regulation of iron ion transport / regulation of erythrocyte differentiation / negative regulation of receptor-mediated endocytosis / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / cellular response to iron ion / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / phagocytic vesicle membrane / positive regulation of immune response / recycling endosome membrane / positive regulation of T cell activation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / learning or memory / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / external side of plasma membrane / lysosomal membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
MHC class I antigen / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Influenza B virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsGras, S. / Nguyen, A.T. / Szeto, C. / Rossjohn, J.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1159272 Australia
National Health and Medical Research Council (NHMRC, Australia)1173871 Australia
CitationJournal: Nat Commun / Year: 2021
Title: CD8 + T cell landscape in Indigenous and non-Indigenous people restricted by influenza mortality-associated HLA-A*24:02 allomorph.
Authors: Hensen, L. / Illing, P.T. / Bridie Clemens, E. / Nguyen, T.H.O. / Koutsakos, M. / van de Sandt, C.E. / Mifsud, N.A. / Nguyen, A.T. / Szeto, C. / Chua, B.Y. / Halim, H. / Rizzetto, S. / ...Authors: Hensen, L. / Illing, P.T. / Bridie Clemens, E. / Nguyen, T.H.O. / Koutsakos, M. / van de Sandt, C.E. / Mifsud, N.A. / Nguyen, A.T. / Szeto, C. / Chua, B.Y. / Halim, H. / Rizzetto, S. / Luciani, F. / Loh, L. / Grant, E.J. / Saunders, P.M. / Brooks, A.G. / Rockman, S. / Kotsimbos, T.C. / Cheng, A.C. / Richards, M. / Westall, G.P. / Wakim, L.M. / Loudovaris, T. / Mannering, S.I. / Elliott, M. / Tangye, S.G. / Jackson, D.C. / Flanagan, K.L. / Rossjohn, J. / Gras, S. / Davies, J. / Miller, A. / Tong, S.Y.C. / Purcell, A.W. / Kedzierska, K.
History
DepositionSep 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: NP peptide from influenza, YFSPIRVTF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0115
Polymers44,9623
Non-polymers492
Water10,701594
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-39 kcal/mol
Surface area18700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.952, 75.775, 89.919
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MHC class I antigen / HLA-A*2402 heavy chain


Mass: 31952.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A411J078
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769
#3: Protein/peptide NP peptide from influenza, YFSPIRVTF


Mass: 1130.315 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: peptide from influenza virus / Source: (synth.) Influenza B virus
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 594 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.43 % / Mosaicity: 0.22 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 19% PEG 3350, 0.2 MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.51→34.915 Å / Num. obs: 64117 / % possible obs: 94 % / Redundancy: 9.8 % / CC1/2: 1 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.014 / Rrim(I) all: 0.045 / Net I/σ(I): 28.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.51-1.549.40.4483050732330.9440.1490.4734.496.2
8.27-34.917.30.02628183840.9990.010.02858.477.7

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F7M

4f7m


Resolution: 1.51→34.915 Å / SU ML: 0.15 / σ(F): 1.33 / Phase error: 20.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2064 3126 4.9 %
Rwork0.1868 --
obs0.1878 63764 93.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: final / Resolution: 1.51→34.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3155 0 2 594 3751
Biso mean--30.85 34.62 -
Num. residues----385
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063434
X-RAY DIFFRACTIONf_angle_d0.8774685
X-RAY DIFFRACTIONf_dihedral_angle_d6.4452792
X-RAY DIFFRACTIONf_chiral_restr0.053473
X-RAY DIFFRACTIONf_plane_restr0.005624
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.53360.26541540.22932786X-RAY DIFFRACTION96
1.5336-1.55870.21961480.20542871X-RAY DIFFRACTION100
1.5587-1.58560.27621330.2042964X-RAY DIFFRACTION100
1.5856-1.61440.23091530.20132942X-RAY DIFFRACTION100
1.6144-1.64550.23731630.20722850X-RAY DIFFRACTION100
1.6455-1.67910.2441390.20592926X-RAY DIFFRACTION100
1.6791-1.71560.26671140.21152653X-RAY DIFFRACTION98
1.7156-1.75550.20241340.20422725X-RAY DIFFRACTION97
1.7555-1.79940.23541620.21152930X-RAY DIFFRACTION100
1.7994-1.8480.23911620.21582885X-RAY DIFFRACTION100
1.848-1.90240.27971540.22752907X-RAY DIFFRACTION100
1.9024-1.96380.4539500.34811101X-RAY DIFFRACTION37
1.9638-2.0340.24131490.212894X-RAY DIFFRACTION99
2.034-2.11540.20041410.19122924X-RAY DIFFRACTION100
2.1154-2.21170.23041540.19922927X-RAY DIFFRACTION100
2.2117-2.32830.2136880.24291699X-RAY DIFFRACTION57
2.3283-2.47410.21311540.19952942X-RAY DIFFRACTION100
2.4741-2.66510.18961660.18832951X-RAY DIFFRACTION100
2.6651-2.93310.21641470.18372979X-RAY DIFFRACTION100
2.9331-3.35730.20051520.16832994X-RAY DIFFRACTION100
3.3573-4.22870.17991540.1552769X-RAY DIFFRACTION92
4.2287-34.9240.13791550.14343019X-RAY DIFFRACTION95

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